Three-dimensional velocity models can enable accurate earthquake location, improved seismic hazard assessment, and can enhance our understanding of geodynamic processes. This is particularly true for areas such as the Aegean, where the crust is marked by active volcanoes as well as shear and rift zones, all of which make this region highly heterogeneous. This work describes the application of local earthquake tomography in order to elucidate the crustal structure of the Aegean. We utilized a dataset of 2,135,625 P arrivals and 1,095,515 S arrivals from 178,676 events recorded across 324 stations. Results indicate that the boundary separating the slow Vp from the fast anomalies at 20–40 km depth is well correlated with the Aegean Moho obtained from receiver functions. A slow Vp (−5%) zone at depths >30 km along the Hellenic arc is likely associated with basal underplating that forms the base of the crust. On the other hand, fast Vp and moderate to high Vp/Vs (1.77–1.92) in the upper-middle crust may indicate evolving metamorphic core complexes. Steeply dipping clusters of earthquakes could highlight pathways of fluid migration from the base to the middle/upper crust, albeit more detailed seismological studies are needed to confirm this interpretation. The 3D velocity model can be also utilized in order to investigate the amount of melt fraction beneath active volcanoes and the influence of fluids on the rupture zone of large earthquakes. Our results show a melt fraction between 4 and 10% beneath active volcanoes, with the largest volume of melt present beneath Santorini caldera. The ruptures zones of 10 large earthquakes (Mw ≥ 6.0), show slow Vp anomalies and moderate to high Vp/Vs (> 1.77), suggesting that these events were likely triggered by weakening of their source zones by fluid activity.